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PubMed2001

Heterologous, splicing-dependent RNA editing in chloroplasts: allotetraploidy provides trans-factors.

RNA editing is unique among post-transcriptional processes in plastids, as it exhibits extraordinary phylogenetic dynamics leading to species-specific editing site patterns. The evolutionary loss of a site is considered to entail the loss of the corresponding nuclear-encoded site-specific factor, which prevents the editing of foreign, i.e. heterologous, sites. We investigated the editing of short 'spliced' and 'unspliced' ndhA gene fragments from spinach in Nicotiana tabacum (tobacco) in vivo using biolistic transformation. Surprisingly, it turned out that the spinach site is edited in the heterologous nuclear background. Furthermore, only exon-exon fusions were edited, whereas intron-containing messages remained unprocessed. A homologue of the spinach site was found to be present and edited in Nicotiana tomentosiformis, representing the paternal parent, but absent from Nicotiana sylvestris, representing the maternal parent of tobacco. Our data show that: (i) the cis-determinants for ndhA editing are split by an intron; (ii) the editing capacity cannot be deduced from editing sites; and (iii) allopolyploidization can increase the editing capacity, which implies that it can influence speciation processes in evolution.

Base Sequence↗
PubMed2001

Environmental impacts and metal exposure of aquatic ecosystems in rivers contaminated by small scale gold mining: the Puyango River basin, southern Ecuador.

Gold mining in the Portovelo-Zaruma district in southern Ecuador is causing considerable environmental impacts; the most important ones are related to the discharge of cyanide, mercury and metal rich tailings into rivers of the Puyango catchment area. Cyanide and metal levels in rivers regularly exceed environmental quality criteria. The contamination impacts biodiversity, with cyanide causing a direct lethal effect on biota close to source and metal contaminants considerably reducing aquatic biodiversity further downstream. It is shown that the prevailing neutral or slightly alkaline conditions of the rivers ensure that metals are mainly associated with sediment. However, elevated metal levels in bottom living larvae collected from contaminated sites suggest that these sediment bound metals are readily bioavailable. Leaching experiments indicate that the relative ease by which metals are taken up by larvae is related to the speciation of sediment associated metals. It is further shown that large amounts of metals, which are bound to suspended sediment under ambient pH conditions, enter the dissolved and directly bioavailable state in more acidic conditions. Metal levels in carnivorous fish were found to be modestly elevated only, with the exception of mercury. Mercury levels exceeded 0.5 mg/kg in fish from both contaminated and uncontaminated sites, showing that both methylation and bioaccumulation of mercury are occurring in the Puyango river basin.

Animals↗
PubMed1976

Rates, patterns, and effectiveness of evolution in multi-level situations.

Evolution is a multi-level process. Both actual evidence and theoretical considerations suggest as a first generalization that evolution both at single levels and in series of increasingly complex levels decelerates with time. Additional evidence, the expected difference between rapid nonadaptive speciation in small populations and effective adaptation in large ones, and analysis of explosive evolution suggest further that effective adaptive evolution occurs primarily in large populations, and that segments of such evolution tend to begin slowly; accelerate, sometimes explosively; and then decelerate. The segments are irregular, and do not occur at regular intervals. However, the explosive evolution of a general adaptation pre-adapts to and is often followed by an explosive radiation of derivative lineages. This description seems to fit the origin and initial radiation of mammals, and the evolutionary history of man and man's cultures.

Animals↗
PubMed2004

Sexual conflict and sexual selection: lost in the chase.

The emergent field of evolutionary biology that studies disparities between the evolutionary interests of alleles expressed in the two sexes, or sexual conflict, promises to offer novel insights into male-female coevolution and speciation. Our theoretical understanding of basic concepts is, however, still incomplete. In a recent perspective paper, Pizzari and Snook provided a framework for understanding sexually antagonistic coevolution and for distinguishing this process from other models of male-female coevolution and suggested an experimental protocol to test for sexually antagonistic coevolution. Here, I show that the framework is flawed, primarily because it is built upon the mistaken assumption that male and female fitness can evolve independently. Further, while the empirical strategy advocated has indeed offered important insights in the past, it does not allow unambiguous discrimination between competing hypotheses.

Animals↗
PubMed2002

The ecology of individuals: incidence and implications of individual specialization.

Most empirical and theoretical studies of resource use and population dynamics treat conspecific individuals as ecologically equivalent. This simplification is only justified if interindividual niche variation is rare, weak, or has a trivial effect on ecological processes. This article reviews the incidence, degree, causes, and implications of individual-level niche variation to challenge these simplifications. Evidence for individual specialization is available for 93 species distributed across a broad range of taxonomic groups. Although few studies have quantified the degree to which individuals are specialized relative to their population, between-individual variation can sometimes comprise the majority of the population's niche width. The degree of individual specialization varies widely among species and among populations, reflecting a diverse array of physiological, behavioral, and ecological mechanisms that can generate intrapopulation variation. Finally, individual specialization has potentially important ecological, evolutionary, and conservation implications. Theory suggests that niche variation facilitates frequency-dependent interactions that can profoundly affect the population's stability, the amount of intraspecific competition, fitness-function shapes, and the population's capacity to diversify and speciate rapidly. Our collection of case studies suggests that individual specialization is a widespread but underappreciated phenomenon that poses many important but unanswered questions.

Animals↗
PubMed2006

New York State urban and rural measurements of continuous PM2.5 mass by FDMS, TEOM, and BAM.

Field evaluations and comparisons of continuous fine particulate matter (PM2,5) mass measurement technologies at an urban and a rural site in New York state are performed. The continuous measurement technologies include the filter dynamics measurement system (FDMS) tapered element oscillating microbalance (TEOM) monitor, the stand-alone TEOM monitor (without the FDMS), and the beta attenuation monitor (BAM). These continuous measurement methods are also compared with 24-hr integrated filters collected and analyzed under the Federal Reference Method (FRM) protocol. The measurement sites are New York City (the borough of Queens) and Addison, a rural area of southwestern New York state. New York City data comparisons between the FDMS TEOM, BAM, and FRM are examined for bias and seasonality during a 2-yr period. Data comparisons for the FDMS TEOM and FRM from the Addison location are examined for the same 2-yr period. The BAM and FDMS measurements at Queens are highly correlated with each other and the FRM. The BAM and FDMS are very similar to each other in magnitude, and both are approximately 25% higher than the FRM filter measurements at this site. The FDMS at Addison measures approximately 9% more mass than the FRM. Mass reconstructions using the speciation trends network filter data are examined to provide insight as to the contribution of volatile species of PM2.5 in the FDMS mass measurement and the fraction that is likely lost in the FRM mass measurement. The reconstructed mass at Queens is systematically lower than the FDMS by approximately 10%.

Air Pollutants, Occupational↗
PubMed2004

Energy gradients and the geographic distribution of local ant diversity.

Geographical diversity gradients, even among local communities, can ultimately arise from geographical differences in speciation and extinction rates. We evaluated three models--energy-speciation, energy-abundance, and area--that predict how geographic trends in net diversification rates generate trends in diversity. We sampled 96 litter ant communities from four provinces: Australia, Madagascar, North America, and South America. The energy-speciation hypothesis best predicted ant species richness by accurately predicting the slope of the temperature diversity curve, and accounting for most of the variation in diversity. The communities showed a strong latitudinal gradient in species richness as well as inter-province differences in diversity. The former vanished in the temperature-diversity residuals, suggesting that the latitudinal gradient arises primarily from higher diversification rates in the tropics. However, inter-province differences in diversity persisted in those residuals--South American communities remained more diverse than those in North America and Australia even after the effects of temperature were removed.

Animals↗
PubMed2004

An FTIR-DRIFT study on river sediment particle structure: implications for biofilm dynamics and pollutant binding.

Diffuse reflectance infrared Fourier transform (DRIFT) spectrometry was applied to a set of sediment samples collected by traps over one and a half years in a mid-mountainous river. Dynamic changes in hydrological and life-cycle conditions generated sediment particles of different C(org) content and organic composition. Periods in the midst of or shortly after flood events left particles poor in C(org) content with spectral features that were enriched in carboxylic and aromatic signals. These are characteristic of terrestrial oxidized vascular plant debris. Low-flow conditions saw the consequent build-up of amide, aliphatic, and polysaccharide moieties as expected for autochthonous biofilm derived material. A peak ratio of two bands representing the alternation of these two types of organic matter showed that flood particle C(org) had a higher affinity for metals than the high C(org) of mature biofilms, probably owing to higher COO- contents in the first. The relative dietary bioavailability of the metals from sediment C(org), which is related to the nutritional value of the substrate, is therefore probably lower in the aftermath of a flood than in prolonged low-flow situations. This needs to be accounted for in future metal speciation and bioavailability modeling approaches.

Adsorption↗
PubMed2005

Adaptive molecular evolution in the opsin genes of rapidly speciating cichlid species.

Cichlid fish inhabit a diverse range of environments that vary in the spectral content of light available for vision. These differences should result in adaptive selective pressure on the genes involved in visual sensitivity, the opsin genes. This study examines the evidence for differential adaptive molecular evolution in East African cichlid opsin genes due to gross differences in environmental light conditions. First, we characterize the selective regime experienced by cichlid opsin genes using a likelihood ratio test format, comparing likelihood models with different constraints on the relative rates of amino acid substitution, across sites. Second, we compare turbid and clear lineages to determine if there is evidence of differences in relative rates of substitution. Third, we present evidence of functional diversification and its relationship to the photic environment among cichlid opsin genes. We report statistical evidence of positive selection in all cichlid opsin genes, except short wavelength-sensitive 1 and short wavelength-sensitive 2b. In all genes predicted to be under positive selection, except short wavelength-sensitive 2a, we find differences in selective pressure between turbid and clear lineages. Potential spectral tuning sites are variable among all cichlid opsin genes; however, patterns of substitution consistent with photic environment-driven evolution of opsin genes are observed only for short wavelength-sensitive 1 opsin genes. This study identifies a number of promising candidate-tuning sites for future study by site-directed mutagenesis. This work also begins to demonstrate the molecular evolutionary dynamics of cichlid visual sensitivity and its relationship to the photic environment.

Animals↗
PubMed2002

Utility of low-copy nuclear gene sequences in plant phylogenetics.

Low-copy nuclear genes in plants are a rich source of phylogenetic information. They hold a great potential to improve the robustness of phylogenetic reconstruction at all taxonomic levels, especially where universal markers such as cpDNA and nrDNA are unable to generate strong phylogenetic hypotheses. Low-copy nuclear genes, however, remain underused in plant phylogenetic studies due to practical and theoretical complications in unraveling the evolutionary dynamics of nuclear gene families. The lack of the universal markers or universal PCR primers of low-copy nuclear genes has also hampered their phylogenetic utility. It has recently become clear that low-copy nuclear genes are particularly helpful in resolving close interspecific relationships and in reconstructing allopolyploidization in plants. Gene markers that are widely, if not universally, useful have begun to emerge. Although utilizing low-copy nuclear genes usually requires extra lab work such as designing PCR primers, PCR-cloning, and/or Southern blotting, rapid accumulation of gene sequences in the databases and advances in cloning techniques have continued to make such studies more feasible. With the growing number of theoretical studies devoted to the gene tree and species tree problem, a solid foundation for reconstructing complex plant phylogenies based on multiple gene trees began to build. It is also realized increasingly that fast evolving introns of the low-copy nuclear genes will provide much needed phylogenetic information around the species boundary and allow us to address fundamental questions concerning processes of plant speciation. Phylogenetic and molecular evolutionary analyses of developmentally important genes will add a new dimension to systematic and evolutionary studies of plant diversity.

Cell Nucleus↗
PubMed2004

Computational aspects of host-parasite phylogenies.

Computational aspects of host-parasite phylogenies form part of a set of general associations between areas and organisms, hosts and parasites, and species and genes. The problem is not new and the commonalities of exploring vicariance biogeography (organisms tracking areas) and host-parasite co-speciation (parasites tracking hosts) have been recognised for some time. Methods for comparing host-parasite phylogenies are now well established and fall within two basic categories defined in terms of the way the data are interpreted in relation to the comparison of host-parasite phylogenies, so-called a posteriori, eg Brooks' Parsimony Analysis (BPA), or a priori, eg reconciled trees and other model-based methods, as implemented in the program TreeMap; the relative merits of the two philosophies inherent in these two approaches remain hotly debated. This paper reviews the computational methods currently available to analyse host-parasite relationships.

Algorithms↗
PubMed2002

Ecology and biogeography of marine parasites.

A review is given of (mainly recent) work on the biodiversity, ecology, biogeography and practical importance of marine parasites. Problems in estimating species numbers have been thoroughly discussed for free-living species, and the main points of these discussions are reviewed here. Even rough estimates of the richness of most parasite groups in the oceans are premature for the following reasons: species numbers of host groups, in particular in the deep sea and the meiofauna, are not known; most host groups have been examined only insufficiently for parasites or not at all; even in some of the best known groups, latitudinal, longitudinal and depth gradients in species richness are only poorly understood or not known at all; effects of hosts on parasite morphology and geographical variation have been studied only in a few cases; there are few studies using techniques of molecular biology to distinguish sibling species. Estimates of species richness in the best known groups, trematodes, monogeneans and copepods of marine fishes, are given. Parasites are found in almost all taxa of eukaryotes, but most parasitic species are concentrated in a few taxa. Important aspects of the ecology of marine parasites are discussed. It is emphasized that host specificity and host ranges should be distinguished, and an index that permits calculation of host specificity is discussed. The same index can be applied to measure site specificity. Central problems in ecology are the importance of interspecific competition and whether equilibrium or non-equilibrium conditions prevail. Marine parasites are among the few groups of organisms that have been extensively examined in this regard. A holistic approach, i.e. application of many methods, has unambiguously shown that metazoan ecto- (and probably endo-) parasites of marine fish live in largely non-saturated niche space under non-equilibrium conditions, i.e. they live in assemblages rather than in communities structured by competition. Nestedness occurs in such assemblages, but it can be explained by characteristics of the species themselves. There is little agreement on which other factors are involved in "structuring" parasite assemblages. Few studies on metapopulations of marine parasites have been made. A new approach, that of fuzzy chaos modelling, is discussed. It is likely that marine parasites are commonly found in metapopulations consisting of many subpopulations, and they are ideally suited to test the predictions of fuzzy chaos. Some recent studies on functional ecology and morphology--especially with regard to host, site and mate finding--are discussed, and attention is drawn to the amazing variety of sensory receptors in some marine parasites. Effects of parasites on hosts, and some studies on the evolution and speciation of marine parasites are discussed as well. A detailed overview of biogeographical studies is given, with respect to latitudinal gradients in species diversity, reproductive strategies and host ranges/specificity. Studies of marine parasites have contributed significantly to giving a non-equilibrium explanation for latitudinal diversity gradients. Recent studies on longitudinal and depth gradients are discussed, as well as parasites in brackish water, parasites as indicators of zoogeographical regions and barriers, and parasites as biological tags. The practical importance of marine parasites in mariculture, as monitors of pollution, agents of human disease, the use of parasites for controlling introduced marine pests, and some related aspects, are also discussed.

Animals↗
PubMed2005

Phylogeography of Balkan wall lizard (Podarcis taurica) and its relatives inferred from mitochondrial DNA sequences.

Wall lizards of the genus Podarcis (Sauria, Lacertidae) comprise 17 currently recognized species in southern Europe, where they are the predominant reptile group. The taxonomy of Podarcis is complex and unstable. Based on DNA sequence data the species of Podarcis falls into four main groups that have substantial geographical conherence (western island group, southwestern group, Italian group and Balkan group). The Balkan species are divided in two subgroups: the subgroup of Podarcis taurica (P. taurica, P. milensis, P. gaigeae and perhaps P. melisellensis), and the subgroup of Podarcis erhardii (P. erhardii and P. peloponnesiaca). We addressed the question of phylogenetic relations among the species of the P. taurica subgroup encountered in Greece, as they can be inferred from partial mtDNA (cyt b and 16S) sequences. Our data support the monophyly of P. taurica subgroup and suggest that P. gaigeae, P. milensis and P. melisellensis form a clade, which thereinafter connects to P. taurica. Within the previous clade, P. gaigeae is more closely related to P. milensis than to P. melisellensis. However, the specimens of P. taurica were subdivided in two different groups. The first one includes the specimens from northeastern Greece, and the other group includes the specimens from the rest of continental Greece and Ionian islands. Because the molecular clock of the cyt b and 16 rRNA genes was not rejected in our model test, it is possible to estimate times of speciation events. Based on the splitting of the island of Crete from Peloponnisos [c. 5 million years ago (Ma)], the evolutionary rate for the cyt b is 1.55% per million years (Myr) and for the 16S rRNA is 0.46% per Myr. These results suggest that the evolutionary history of P. taurica in Greece is more complex than a single evolutionary invasion. The data analysed, stress the need for a reconsideration of the evolutionary history of Greek Podarcis species and help overcome difficulties that classical taxonomy has encountered at both the species level.

Animals↗
PubMed2024

Assessing the emergence time of SARS-CoV-2 zoonotic spillover.

Understanding the evolution of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) and its relationship to other coronaviruses in the wild is crucial for preventing future virus outbreaks. While the origin of the SARS-CoV-2 pandemic remains uncertain, mounting evidence suggests the direct involvement of the bat and pangolin coronaviruses in the evolution of the SARS-CoV-2 genome. To unravel the early days of a probable zoonotic spillover event, we analyzed genomic data from various coronavirus strains from both human and wild hosts. Bayesian phylogenetic analysis was performed using multiple datasets, using strict and relaxed clock evolutionary models to estimate the occurrence times of key speciation, gene transfer, and recombination events affecting the evolution of SARS-CoV-2 and its closest relatives. We found strong evidence supporting the presence of temporal structure in datasets containing SARS-CoV-2 variants, enabling us to estimate the time of SARS-CoV-2 zoonotic spillover between August and early October 2019. In contrast, datasets without SARS-CoV-2 variants provided mixed results in terms of temporal structure. However, they allowed us to establish that the presence of a statistically robust clade in the phylogenies of gene S and its receptor-binding (RBD) domain, including two bat (BANAL) and two Guangdong pangolin coronaviruses (CoVs), is due to the horizontal gene transfer of this gene from the bat CoV to the pangolin CoV that occurred in the middle of 2018. Importantly, this clade is closely located to SARS-CoV-2 in both phylogenies. This phylogenetic proximity had been explained by an RBD gene transfer from the Guangdong pangolin CoV to a very recent ancestor of SARS-CoV-2 in some earlier works in the field before the BANAL coronaviruses were discovered. Overall, our study provides valuable insights into the timeline and evolutionary dynamics of the SARS-CoV-2 pandemic.

Animals↗
PubMed2002

A spatially explicit neutral model of beta-diversity in tropical forests.

To represent species turnover in tropical rain forest, we use a neutral model where a tree's fate is not affected by what species it belongs to, seeds disperse a limited distance from their parents, and speciation is in equilibrium with random extinction. We calculate the similarity function, the probability F(r) that two trees separated by a distance r belong to the same species, assuming that the dispersal kernel P(r), the distribution of seeds about their parents and the prospects of mortality and reproduction, are the same for all trees regardless of their species. If P(r) is radially symmetric Gaussian with mean-square dispersal distance sigma, F(r) can be expressed in closed form. If P(r) is a radially symmetric Cauchy distribution, then, in two-dimensional space, F(r) is proportional to 1/r for large r. Analytical results are compared with individual-based simulations, and the relevance to field observations is discussed.

Ecosystem↗
PubMed2004

Laboratory mating trials indicate incipient speciation by sexual selection among populations of the cichlid fish Pseudotropheus zebra from Lake Malawi.

It has been suggested that sexual selection may have played a major role in the rapid evolution of hundreds of species of cichlid fishes in Lake Malawi. We report the results of a laboratory test of assortative mating among Lake Malawi cichlid fishes from five closely related geographical populations differing in male courtship colour. Paternity of clutches was tested using microsatellite DNA typing of offspring. Out of 1955 offspring typed, 1296 (66.3%) were sired by the male from the same population as the female, which is more than three times the rate expected if females do not differentiate among males of the different populations (20%). This result indicates that mate preferences of geographical races are strongly differentiated, consistent with the races representing incipient geographical species diverging under sexual selection exerted by female preferences for different male courtship colours.

Animals↗
PubMed2004

The tobacco mouse and its relatives: a "tail" of coat colors, chromosomes, hybridization and speciation.

The article reviews over 30 years' study of the chromosomal variation of the western house mice (Mus musculus domesticus) from the neighboring valleys of Poschiavo and Valtellina on the Swiss-Italian border. This is done in the context of the social and political history of this area, on the grounds that mice, as commensals, are influenced by human history. The chromosomal study of mice in this area was initiated because their unusual black coat color led a 19th century naturalist to describe the "tobacco mice" from Val Poschiavo as a separate species (Mus poschiavinus). The special coloration of the Val Poschiavo mice is matched by their chromosomes: they have 26 chromosomes instead of the usual 40. The Val Poschiavo mice are not a separate species according to the Biological Species Concept; instead they constitute a chromosome race (the "Poschiavo", POS) that is related to other races with reduced chromosome numbers that occur in N Italy (of which only those races in Val Poschiavo and Upper Valtellina have black coats). A phylogenetic analysis of mitochondrial DNA sequences suggests that the lineage of chromosome races found in N Italy was not formed during an extreme population bottleneck, although such bottlenecks have apparently occurred during the origin of individual races and certainly have influenced single populations. In one small, isolated population in Valtellina (Migiondo), two chromosome races (the POS and the "Upper Valtellina", UV, 2n = 24) became reproductively isolated from each other. In another small population (Sernio) bottlenecking led to fixation of a hybrid form with the UV karyotype and coat color, but with allozyme and microsatellite alleles characteristic of mice with the standard 40-chromosome karyotype. Two of the chromosome races in Valtellina (the UV and the "Mid Valtellina", MV, 2n = 24) also appear to be the product of hybridization. The dynamic history and patchy distribution of the house mouse chromosome races in Val Poschiavo and Valtellina in part reflects extinction-recolonization events; the formation of the UV and MV races and the introduction of the pale brown Standard race mice are believed to reflect such events. Dynamism in the chromosomal constitution of single populations is also evident from 25 years of data on the population in Migiondo. Due to change in agricultural practices, house mice in Valtellina and Val Poschiavo are becoming rarer, which is likely to have further impacts on the distribution and characteristics of the chromosome races in this area.

Animals↗
PubMed1998

Molecular evolution of the globin gene cluster E in two distantly related midges, Chironomus pallidivittatus and C. thummi thummi.

We have studied the evolutionary dynamics of a cluster of insect globin genes by comparing the organization and sequence of the gene group in two distantly related species, Chironomus pallidivittatus and C. t. thummi. Although the general architecture of the globin gene cluster has been conserved, we have found an additional, previously undescribed gene (named Cpa F) in C. pallidivittatus which shows signs of accelerated sequence evolution at nonsynonymous codon positions. This new gene is clearly functional, as demonstrated by Northern analysis. Comparison of paralogous and orthologous genes reveals patterns of intraspecific sequence homogenization. The head-to-head-oriented globin 3 and 4 gene pairs in C. t. thummi and the gb 4 gene pair in C. pallidivittatus have been efficiently homogenized, probably by gene conversion, in their promoter and coding regions. Inverted transcriptional orientation seems to favor efficient conversion. The orthologous genes from C. t. thummi and C. pallidivittatus reveal different levels of sequence conservation, ranging from 85.3 to 94.7% amino acid identity. Surprisingly, globin gene E, for which up to now no corresponding protein has been detected in the larval hemolymph of C. t. thummi, shows the highest degree of interspecies sequence conservation. This points to an essential, as yet unknown function of this globin. The usefulness of globin gene comparisons for dating speciation events in Chironomus is discussed.

Amino Acid Sequence↗